rs201868215

Variant names:

• chr8-1565865-C-T
• rs201868215
• NM_001346810.2:c.1413C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-1565865-C-T
• chr8-1565865-C-G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_001346810.2(DLGAP2):​c.1413C>T​(p.Ile471Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,610,760 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0016 (5 hom.)
• Consequence: DLGAP2 NM_001346810.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.795
• Publications: 0 publications found

Genes affected

DLGAP2 (HGNC:2906): (DLG associated protein 2) The product of this gene is a membrane-associated protein that may play a role in synapse organization and signalling in neuronal cells. This gene is biallelically expressed in the brain, however, only the paternal allele is expressed in the testis (PMID:18055845). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2014]

DLGAP2-AS1 (HGNC:50467): (DLGAP2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.017).
• BP6: Variant 8-1565865-C-T is Benign according to our data. Variant chr8-1565865-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2658292.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.795 with no splicing effect.
• BS2: High AC in GnomAd4 at 210 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001346810.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	NM_001346810.2	MANE Select	c.1413C>T	p.Ile471Ile	synonymous	Exon 6 of 15	NP_001333739.1	A0A1B0GTN4
	DLGAP2-AS1	NR_103863.1		n.358-127G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLGAP2	ENST00000637795.2	TSL:5 MANE Select	c.1413C>T	p.Ile471Ile	synonymous	Exon 6 of 15	ENSP00000489774.1	A0A1B0GTN4
	DLGAP2	ENST00000520901.5	TSL:1	c.1221C>T	p.Ile407Ile	synonymous	Exon 2 of 10	ENSP00000430563.3	H0YBY6
	DLGAP2	ENST00000421627.7	TSL:5	c.1410C>T	p.Ile470Ile	synonymous	Exon 6 of 15	ENSP00000400258.3	Q9P1A6-1

Frequencies

GnomAD3 genomes AF: 0.00139 AC: 211 AN: 152194 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000386

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00270

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.00114 AC: 276 AN: 242730 AF XY: 0.00111

Gnomad AFR exome AF: 0.000269

Gnomad AMR exome AF: 0.000207

Gnomad ASJ exome AF: 0.000101

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00170

Gnomad NFE exome AF: 0.00178

Gnomad OTH exome AF: 0.00101

GnomAD4 exome AF: 0.00164 AC: 2391 AN: 1458448 Hom.: 5 Cov.: 33 AF XY: 0.00167 AC XY: 1208 AN XY: 725200

African (AFR) AF: 0.000389 AC: 13 AN: 33386

American (AMR) AF: 0.000203 AC: 9 AN: 44278

Ashkenazi Jewish (ASJ) AF: 0.000153 AC: 4 AN: 26080

East Asian (EAS) AF: 0.00 AC: 0 AN: 39516

South Asian (SAS) AF: 0.000818 AC: 70 AN: 85548

European-Finnish (FIN) AF: 0.00148 AC: 79 AN: 53204

Middle Eastern (MID) AF: 0.000352 AC: 2 AN: 5674

European-Non Finnish (NFE) AF: 0.00194 AC: 2150 AN: 1110478

Other (OTH) AF: 0.00106 AC: 64 AN: 60284

GnomAD4 genome AF: 0.00138 AC: 210 AN: 152312 Hom.: 0 Cov.: 33 AF XY: 0.000994 AC XY: 74 AN XY: 74468

African (AFR) AF: 0.000385 AC: 16 AN: 41568

American (AMR) AF: 0.0000654 AC: 1 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4822

European-Finnish (FIN) AF: 0.000471 AC: 5 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00270 AC: 184 AN: 68030

Other (OTH) AF: 0.000473 AC: 1 AN: 2114

Alfa AF: 0.00169 Hom.: 0

Bravo AF: 0.00104

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	0.85
DANN	Benign	0.78
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201868215; hg19: chr8-1514031;